// ------------------------------------------------------------------------
void createLabelImage(const SeriesTransform &series,
const ImageType::Pointer &reference,
const LevelSetType::Pointer &levelSet,
const std::vector<int> &roiOffset,
ImageType::Pointer &label,
unsigned int instance)
{
// initialise the label image
createOutput(series.images[instance], label);
// create the level set interpolator
typedef itk::LinearInterpolateImageFunction<LevelSetType> InterpolatorType;
InterpolatorType::Pointer interpolator = InterpolatorType::New();
interpolator->SetInputImage(levelSet);
// iterate through the output
itk::ImageRegionIterator<ImageType> it(label, label->GetLargestPossibleRegion());
it.GoToBegin();
while(!it.IsAtEnd())
{
ImageType::IndexType index = it.GetIndex();
ImageType::PointType p1, p2;
// get the point in the level set space
label->TransformIndexToPhysicalPoint(index, p1);
transformPointToPatient(reference, series, roiOffset, p1, p2);
// interpolate the level set value
if(interpolator->IsInsideBuffer(p2))
{
float val = interpolator->Evaluate(p2);
if(val >= 0) it.Set(1);
}
++it;
}
}
int main (int argc, char **argv)
{
int verbose=0,clobber=0;
int order=2;
static struct option long_options[] = {
{"verbose", no_argument, &verbose, 1},
{"quiet", no_argument, &verbose, 0},
{"clobber", no_argument, &clobber, 1},
{"order", required_argument, 0, 'o'},
{0, 0, 0, 0}
};
for (;;) {
/* getopt_long stores the option index here. */
int option_index = 0;
int c = getopt_long (argc, argv, "vo:", long_options, &option_index);
/* Detect the end of the options. */
if (c == -1) break;
switch (c)
{
case 0:
break;
case 'o':
order=atoi(optarg);break;
case 'v':
cout << "Version: 0.1" << endl;
return 0;
case '?':
/* getopt_long already printed an error message. */
default:
show_usage (argv[0]);
return 1;
}
}
if((argc - optind) < 3) {
show_usage (argv[0]);
return 1;
}
std::string in_volume=argv[optind];
std::string in_obj=argv[optind+1];
std::string out_csv=argv[optind+2];
if (!clobber && !access(out_csv.c_str(), F_OK))
{
cerr << out_csv.c_str() << " Exists!" << endl;
return 1;
}
try
{
itk::ObjectFactoryBase::RegisterFactory(itk::MincImageIOFactory::New());
itk::ImageFileReader<minc::image3d >::Pointer reader = itk::ImageFileReader<minc::image3d >::New();
//initializing the reader
reader->SetFileName(in_volume.c_str());
reader->Update();
minc::image3d::Pointer in=reader->GetOutput();
std::cout<<"Building BSpline interpolator , order="<<order<<std::endl;
InterpolatorType::Pointer interpolator = InterpolatorType::New();
interpolator->SetSplineOrder(order);
interpolator->SetInputImage(in);
std::ofstream output(out_csv.c_str());
VIO_File_formats format;
object_struct **object_list;
int n_objects=0;
//bicpl sucks!
if( input_graphics_file( (char*)in_obj.c_str(), &format, &n_objects,
&object_list ) != VIO_OK )
{
std::cerr << " Error reading "<<in_obj.c_str() << std::endl;
return 1;
}
//const int segment_length=10;
std::vector<minc::tag_point> lines;
std::vector<int> line_index;
std::cout<<"Processing "<<n_objects<<" objects"<<std::endl;
output<<"x,y,z,v"<<std::endl;
for(int i=0;i< n_objects;i++ )
{
if( get_object_type( object_list[i] ) == POLYGONS )
{
polygons_struct *polygons;
polygons = get_polygons_ptr(object_list[i]);
/*object_struct * lobj= create_object( LINES );
lines_struct * lines = get_lines_ptr(lobj);
initialize_lines( lines, WHITE );
lines->n_points = polygons->n_items*segment_length;
ALLOC( lines->points, lines->n_points );*/
for(int pnt=0;pnt< polygons->n_points;pnt++ )
{
VIO_Point p_=polygons->points[pnt];//seeding point
minc::tag_point p_orig,p;
p_orig[0]=p_.coords[0];p_orig[1]=p_.coords[1];p_orig[2]=p_.coords[2];
//line_index.push_back(lines.size());
//lines.push_back(p_orig);
p=p_orig;
double _in=interpolator->Evaluate(p);
/* polygons->points[pnt].coords[0]=p[0];
polygons->points[pnt].coords[1]=p[1];
polygons->points[pnt].coords[2]=p[2];*/
//int size = GET_OBJECT_SIZE( *polygons, poly );
//if(size<3) continue; //?
/* p1=polygons->points[POINT_INDEX( polygons->end_indices, poly, 0 )];
p2=polygons->points[POINT_INDEX( polygons->end_indices, poly, 1 )];
p3=polygons->points[POINT_INDEX( polygons->end_indices, poly, 2 )];*/
/*
std::cout<<poly<<"\t"<<POINT_INDEX( polygons->end_indices, poly, 0 )<<" "
<<POINT_INDEX( polygons->end_indices, poly, 1 )<<" "
<<POINT_INDEX( polygons->end_indices, poly, 2 )<<std::endl;*/
//std::cout<<poly<<"\t"<<p1.coords[0]<<" "<<p1.coords[1]<<" "<<p1.coords[2]<<std::endl;
//center
output<<p[0]<<","<<p[1]<<","<<p[2]<<","<<
_in<<std::endl;
}
}
}
//int status = output_graphics_file( (char*)out_objf.c_str(), format,n_objects, object_list );
//free up memory
delete_object_list( n_objects, object_list );
//return( status != OK );
/*
//outputting lines
FILE *fp=fopen(out_objf.c_str(),"w");
// IL want to write in binary
fprintf(fp,"L 0.1 %d\n",lines.size());
//WRITING cordinates
for (int i=0;i<lines.size();i++) {
fprintf(fp,"%f %f %f\n",lines[i][0],lines[i][1],lines[i][2]);
}
fprintf(fp,"%d\n1 ",line_index.size()); //1 color per line
for (int i=0;i<line_index.size();i++) { //random colors
fprintf(fp,"%f %f %f 1.0\n",rand()/(double)RAND_MAX,rand()/(double)RAND_MAX,rand()/(double)RAND_MAX);
}
for (int i=0;i<line_index.size();i++) {
if(i<(line_index.size()-1))
fprintf(fp,"%d ",line_index[i+1]);
else
fprintf(fp,"%d ",lines.size());//last line lasts untill the end
}
fprintf(fp,"\n");
for (int i=0;i<line_index.size();i++)
{
int end=i<(line_index.size()-1)?line_index[i+1]:lines.size();
for(int j=line_index[i];j<end;j++)
fprintf(fp," %d",j);
fprintf(fp,"\n");
}
fclose(fp);*/
} catch (const minc::generic_error & err) {
cerr << "Got an error at:" << err.file () << ":" << err.line () << endl;
return 1;
}
return 0;
};